AMBER Archive (2009)

Subject: Re: [AMBER] Creating conditions for biased MD

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Apr 21 2009 - 16:49:14 CDT

I was not referring to the charge. I meant the warnings about building
the improper torsion parameters. I misunderstood the warnings, i
thought they were related to the imposed torsions and was wondering
whether the impose command was incorrectly constructed. Sorry
francesco

On Tue, Apr 21, 2009 at 11:32 PM, Carlos Simmerling
<carlos.simmerling_at_gmail.com> wrote:
> hi Francesco- what's your question? I'm not sure what you're asking.
> about the warnings? these are probably ok unless you want it neutral.
> carlos
>
>
> On Tue, Apr 21, 2009 at 5:29 PM, Francesco Pietra <chiendarret_at_gmail.com> wrote:
>> I must apologize for not having looked at the leap.log before. The
>> relevant portion of the log:
>>
>>> impose model3 { 225 226 227 228 229 230 } { { "N" "CA" "C" "N" -40.0 } { "C" "N" "CA" "C" -60.0 } }
>>> saveamberparm model3 impose_pore.prmtop impose_pore.inpcrd
>> Checking Unit.
>> WARNING: The unperturbed charge of the unit: 4.999220 is not zero.
>>
>>  -- ignoring the warning.
>>
>> Building topology.
>> Building atom parameters.
>> Building bond parameters.
>> Building angle parameters.
>> Building proper torsion parameters.
>> Building improper torsion parameters.
>>  ** Warning: No sp2 improper torsion term for  NA-CA-CN-CB
>>        atoms are: NE1 CZ2 CE2 CD2
>>  ** Warning: No sp2 improper torsion term for  C*-CN-CB-CA
>>        atoms are: CG CE2 CD2 CE3
>>  ** Warning: No sp2 improper torsion term for  NA-CA-CN-CB
>>        atoms are: NE1 CZ2 CE2 CD2
>>  ** Warning: No sp2 improper torsion term for  C*-CN-CB-CA
>>        atoms are: CG CE2 CD2 CE3
>>  ** Warning: No sp2 improper torsion term for  NA-CA-CN-CB
>>        atoms are: NE1 CZ2 CE2 CD2
>>  ** Warning: No sp2 improper torsion term for  C*-CN-CB-CA
>>        atoms are: CG CE2 CD2 CE3
>>
>> I took the "atomname" specification from the amber archive
>> http://structbio.vanderbilt.edu/archives/amber-archive/2006/2387.php
>>
>> francesco
>>
>>
>>
>> On Tue, Apr 21, 2009 at 9:44 PM, Carlos Simmerling
>> <carlos.simmerling_at_gmail.com> wrote:
>>> I was thinking you could do that if it was only the helix, and I meant
>>> to build a perfect helix from sequence. not sure if impose works when
>>> reading a pdb. I meant to build the helix alone and use that for the
>>> reference, but if the system is more complicated then you should
>>> probably use restraints.
>>>
>>>
>>> On Tue, Apr 21, 2009 at 2:40 PM, Francesco Pietra <chiendarret_at_gmail.com> wrote:
>>>> On Mon, Apr 20, 2009 at 8:46 PM, Carlos Simmerling
>>>> <carlos.simmerling_at_gmail.com> wrote:
>>>>> I think it might be easier with dihedral angle restraints. it depends
>>>>> on the rest of the system- if it's just the one helix, you could use
>>>>> the impose command in leap to make a continuous helix as a reference
>>>>> for SMD.
>>>>
>>>> I begun from the last suggestion, recreating the protein (made of
>>>> capped helices which had been before isolated from the whole protein),
>>>> with commands "model1  = loadpdb" "model2 = load pdb" (where the two
>>>> models had been aligned before)  and "model3 = combine" the protein
>>>> was inserted into a lipidic membrane.
>>>>
>>>> Then command
>>>>
>>>> impose model3 { 225 226 227 228 229 230 }  {  {  "N" "CA" "C" "N"
>>>> -40.0 }  {  "C" "N" "CA" "C" -60.0 } }
>>>>
>>>> Then, with command "solvatebox" it was hydrated. The prmtop and inpcrd
>>>> opened in a viewer, WAT and lipid removed, the bent helix looks like
>>>> (grossly) unaffected. The bending angle is still ca 40 degrees.
>>>>
>>>> Should straightening of the helix have been expected at this stage or
>>>> the impose command will be felt on running MD simulations? Or, have i
>>>> misunderstood everything?
>>>>
>>>> thanks for having a look at this message
>>>>
>>>> francesco
>>>>
>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Mon, Apr 20, 2009 at 1:31 PM, Francesco Pietra <chiendarret_at_gmail.com> wrote:
>>>>>> Carlos: late in thanking you. I had to fix hardware and software problems.
>>>>>>
>>>>>> Complex:
>>>>>>
>>>>>> phi Gly227C  Gly228N  Gly228CA Gly228C  ca 78 degrees (positive)
>>>>>>
>>>>>> psi Gly228N  Gly228CA  Gly228C  Gln229N  -19 degrees
>>>>>>
>>>>>> In a cartoon view, two cylinders make an angle of ca 40 degrees,
>>>>>> interconnected by 227 228. I would like to approximately straighten
>>>>>> that, to get a continuous cylinder. In a helix view, phi should be
>>>>>> turned anticlockwise to reach at least the value -80 degrees (the
>>>>>> value of corresponding nearby dihedral is just -80 degrees, while
>>>>>> farther away it takes normal values, -57 degrees). psi, at least, has
>>>>>> the correct sign.
>>>>>>
>>>>>> The bent helix is capped on both sides, but there are other similar,
>>>>>> capped helices around, so that I guess the work should be carried out
>>>>>> on the whole model. If I could restrain the capping groups alone of
>>>>>> the bent helix (while finding a way that helicity, where correct, is
>>>>>> conserved) I could imagine that straightening could occur. Otherwise,
>>>>>> if all amino acids, except 227 228 of the bent helix, are restrained,
>>>>>> how could the helix get straightened? Is that a task for SMD at all?
>>>>>>
>>>>>> thanks
>>>>>> francesco
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Mon, Mar 30, 2009 at 1:56 PM, Carlos Simmerling
>>>>>> <carlos.simmerling_at_gmail.com> wrote:
>>>>>>> francesco, I think dihedral restraints may be the only way to go without a
>>>>>>> helical ref structure. you'd definitely want to also restrain all other
>>>>>>> residues in this helix to maintain it, or else you might just move the bend.
>>>>>>> when changing the restraints over time, give thought to which direction to
>>>>>>> rotate, which depends on the initial conformation of the Gly residues, if
>>>>>>> they are currently adopting positive phi values then it's more complex than
>>>>>>> just going from pp2 to alpha, for example, where you can just reduce psi.
>>>>>>>
>>>>>>> On Mon, Mar 30, 2009 at 6:16 AM, Francesco Pietra <chiendarret_at_gmail.com>wrote:
>>>>>>>
>>>>>>>> Hi:
>>>>>>>> I would like to modify the conformation of a protein at one helix,
>>>>>>>> which is bent at a region of three amino acids, Ile, Gly, Gly. Viewed
>>>>>>>> in cartoon representation, it is constituted of two straight portions
>>>>>>>> interconnected through a largely non helical set of the three amino
>>>>>>>> acids.
>>>>>>>>
>>>>>>>> I would appreciate suggestions how to get the three aa taking part to
>>>>>>>> the well ordered helical conformation, so that what is now (in
>>>>>>>> cartoon) two straight portions interconnected by something like a loop
>>>>>>>> becomes a wholly straitened motif. Rotation about dihedrals? Make the
>>>>>>>> process with the isolated helix or in the whole context of the
>>>>>>>> protein?
>>>>>>>>
>>>>>>>> I guess that steered MD (on which I have no experience) is the
>>>>>>>> approach in Amber, though I wonder how to provide the target.
>>>>>>>> Possibly, any biased MD should be carried out in explicit medium. In
>>>>>>>> my hands, continuum models were unsuccessful with this protein.
>>>>>>>>
>>>>>>>> If these are not such naive questions to merit attention, thanks
>>>>>>>>
>>>>>>>> francesco pietra
>>>>>>>>
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